A few random thoughts:
Everything is very much bigger than in the current map. Like even check out disposals.
http://goonhub.com/maps/cogmap2#l=160,119,1
What is currently just part of maintenance is now far more expansive. It'll be interesting to see how this effects the game in terms of how people play.
Two mining shuttles? Isn't that a bit overkill for a place that is pretty much redundant?
More escape shuttles.. will they work in this map?
The chaplain with the a handheld mic is a hilarious idea. PREACH BROTHERS.
Also has it seems the chapel is now a multi-purpose area, working for court cases aswell? If that's the case then i'd make the courtroom/chapel more integrated, because currently it looks like a chapel with a prosecution booth latched onto it.
Where is the market/space traders located? If that's yet to be worked in, place it near QM, so you have a money spending hub.
The armory is a bit of a quandary. You've gone for high alert, but no lockers. This on one hand takes power away from the EMAG, which I personally think is a little overpowered to begin with and is a smart move, but on the other hand, any ol' smuck with hacking skills (i.e: Every single player) can bust their way into the armory. I'd suggest that there should be a lock down button, similar to the bridge lockdown. The lockdown button is located in the Hos' room and the AI can press it when the alarm beeps or w/e. Tie in the lockdown button and the infrared beam into the mainframe, that way hacking could be actually useful. disabling both the lockdown and the alarm with your pda would be fairly badass.